52 Result(s)
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Life Sciences
Evolutionary Biology
Plant Genetics and Genomics
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Article
Open AccessGlobal nucleosome occupancy in yeast
Although eukaryotic genomes are generally thought to be entirely chromatin-associated, the activated PHO5 promoter in yeast is largely devoid of nucleosomes. We systematically evaluated nucleosome occupancy in ye...
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Network security and data integrity in academia: an assessment and a proposal for large-scale archiving
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Open AccessA low-cost open-source SNP genoty** platform for association map** applications
Association map** aimed at identifying DNA polymorphisms that contribute to variation in complex traits entails genoty** a large number of single-nucleotide polymorphisms (SNPs) in a very large panel of in...
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Open AccessFine scale structural variants distinguish the genomes of Drosophila melanogaster and D. pseudoobscura
A primary objective of comparative genomics is to identify genomic elements of functional significance that contribute to phenotypic diversity. Complex changes in genome structure (insertions, duplications, re...
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Open AccessLarge-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses
Transcriptional cis-regulatory modules (for example, enhancers) play a critical role in regulating gene expression. While many individual regulatory elements have been characterized, they have never been analyzed...
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Open AccessRNA polymerase map** during stress responses reveals widespread nonproductive transcription in yeast
The use of genome-wide RNA abundance profiling by microarrays and deep sequencing has spurred a revolution in our understanding of transcriptional control. However, changes in mRNA abundance reflect the combin...
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Open AccessSelective Pressure to Increase Charge in Immunodominant Epitopes of the H3 Hemagglutinin Influenza Protein
The evolutionary speed and the consequent immune escape of H3N2 influenza A virus make it an interesting evolutionary system. Charged amino acid residues are often significant contributors to the free energy o...
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Open AccessDeep sequencing on genome-wide scale reveals the unique composition and expression patterns of microRNAs in develo** pollen of Oryza sativa
Pollen development in flowering plants requires strict control of the gene expression program and genetic information stability by mechanisms possibly including the miRNA pathway. However, our understanding of...
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Why rodent pseudogenes refuse to retire
A new study in this issue of Genome Biology sheds light on why some pseudogenes persist in rodent, and other mammalian, genomes.
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Open AccessGenome of the long-living sacred lotus (Nelumbo nucifera Gaertn.)
Sacred lotus is a basal eudicot with agricultural, medicinal, cultural and religious importance. It was domesticated in Asia about 7,000 years ago, and cultivated for its rhizomes and seeds as a food crop. It ...
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Erratum to: Characterization of a genome-specific Gypsy-like retrotransposon sequence and development of a molecular marker specific for Dasypyrum villosum (L.)
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Open AccessArchitecture of epigenetic reprogramming following Twist1-mediated epithelial-mesenchymal transition
Epithelial-mesenchymal transition (EMT) is known to impart metastasis and stemness characteristics in breast cancer. To characterize the epigenetic reprogramming following Twist1-induced EMT, we characterized ...
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Open AccessGenome-wide analysis of light-regulated alternative splicing mediated by photoreceptors in Physcomitrella patens
Light is one of the most important factors regulating plant growth and development. Light-sensing photoreceptors tightly regulate gene expression to control photomorphogenic responses. Although many levels of ...
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Open AccessNew genes drive the evolution of gene interaction networks in the human and mouse genomes
The origin of new genes with novel functions creates genetic and phenotypic diversity in organisms. To acquire functional roles, new genes must integrate into ancestral gene-gene interaction (GGI) networks. Th...
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Open AccessGenomic legacy of the African cheetah, Acinonyx jubatus
Patterns of genetic and genomic variance are informative in inferring population history for human, model species and endangered populations.
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Open AccessChallenges and emerging directions in single-cell analysis
Single-cell analysis is a rapidly evolving approach to characterize genome-scale molecular information at the individual cell level. Development of single-cell technologies and computational methods has enable...
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Open AccessData normalization considerations for digital tumor dissection
In a recently published article in Genome Biology, Li and colleagues introduced TIMER, a gene expression deconvolution approach for studying tumor-infiltrating leukocytes (TILs) in 23 cancer types profiled by The...
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Open AccessPerfectly matched 20-nucleotide guide RNA sequences enable robust genome editing using high-fidelity SpCas9 nucleases
High-fidelity SpCas9 variants (eSpCas9 and SpCas9-HF1) have been engineered to reduce off-target effects. We found that changes in guide RNA length induced significant reductions in the editing activities of S...
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Open AccessLong-term balancing selection contributes to adaptation in Arabidopsis and its relatives
In contrast to positive selection, which reduces genetic variation by fixing beneficial alleles, balancing selection maintains genetic variation within a population or species and plays crucial roles in adapta...
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Open AccessAdaptation of Arabidopsis thaliana to the Yangtze River basin
Organisms need to adapt to keep pace with a changing environment. Examining recent range expansion aids our understanding of how organisms evolve to overcome environmental constraints. However, how organisms a...
